Opened 5 years ago

Closed 5 years ago

#3235 closed defect (duplicate)

Could not start space navigator

Reported by: ed.luk@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: General Controls Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-19.4.0-x86_64-i386-64bit
ChimeraX Version: 0.94 (2020-04-22)
Description
When I try to use the 'device snav ON' command to turn on my space mouse, I get this error: 
Could not start space navigator.

cannot import name '_spacenavigator' from 'chimerax.spacenavigator' (/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/chimerax/spacenavigator/__init__.py)


Log:
UCSF ChimeraX version: 0.94.dev202004220145 (2020-04-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> close

> device snav true

Could not start space navigator.  
  
cannot import name '_spacenavigator' from 'chimerax.spacenavigator'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/spacenavigator/__init__.py)  

> open 1I7W

1i7w title:  
Beta-catenin/phosphorylated E-cadherin complex [more info...]  
  
Chain information for 1i7w #1  
---  
Chain | Description  
A C | β-catenin  
B D | epithelial-cadherin  
  
Non-standard residues in 1i7w #1  
---  
CL — chloride ion  
ZN — zinc ion  
  
  

> open 1I7X

1i7x title:  
Beta-catenin/E-cadherin complex [more info...]  
  
Chain information for 1i7x #2  
---  
Chain | Description  
A C | β-catenin  
B D | epithelial-cadherin  
  
  

> hide atoms

> show ribbons

> hide solvent

> hide #2 /C/D target c

> hide #1 /C/D target c

> set bgColor grey

> color #1 /A hot pink

> color #1 /B cyan

> color #2 /A rgb(255,255,0)

> color #2 /B rgb(255,0,0)

> mmaker #2:134-664 to #1:167-662

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1i7w, chain C (#1) with 1i7x, chain C (#2), sequence alignment
score = 2482.6  
RMSD between 451 pruned atom pairs is 0.731 angstroms; (across all 482 pairs:
0.994)  
  

> cartoon style #1 #2 width 3 thickness 2

> cartoon style #1 #2 width 3

> cartoon style #1 #2 thickness 1

> show #1/A :cys #2/A :cys

> style #1/A :cys #2/A :cys sphere

Changed 132 atom styles  

> color #1/A :cys #2/A :cys blue

> show #1/A:435,312 #1/B

> style #1/A:435,312 sphere

Changed 18 atom styles  

> color #1/A:435,312 red

> set bgColor black

> hide /A/D

> cle

Unknown command: cle  

> close

> close

> device snav true

Could not start space navigator.  
  
cannot import name '_spacenavigator' from 'chimerax.spacenavigator'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/spacenavigator/__init__.py)  

> open 1I7W

1i7w title:  
Beta-catenin/phosphorylated E-cadherin complex [more info...]  
  
Chain information for 1i7w #1  
---  
Chain | Description  
A C | β-catenin  
B D | epithelial-cadherin  
  
Non-standard residues in 1i7w #1  
---  
CL — chloride ion  
ZN — zinc ion  
  
  

> open 1I7X

1i7x title:  
Beta-catenin/E-cadherin complex [more info...]  
  
Chain information for 1i7x #2  
---  
Chain | Description  
A C | β-catenin  
B D | epithelial-cadherin  
  
  

> hide atoms

> show ribbons

> hide solvent

> hide #2 /C/D target c

> hide #1 /C/D target c

> set bgColor grey

> color #1 /A hot pink

> color #1 /B cyan

> color #2 /A rgb(255,255,0)

> color #2 /B rgb(255,0,0)

> mmaker #2:134-664 to #1:167-662

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 1i7w, chain C (#1) with 1i7x, chain C (#2), sequence alignment
score = 2482.6  
RMSD between 451 pruned atom pairs is 0.731 angstroms; (across all 482 pairs:
0.994)  
  

> cartoon style #1 #2 width 3 thickness 2

> cartoon style #1 #2 width 3

> cartoon style #1 #2 thickness 1

> show #1/A :cys #2/A :cys

> style #1/A :cys #2/A :cys sphere

Changed 132 atom styles  

> color #1/A :cys #2/A :cys blue

> show #1/A:435,312 #1/B

> style #1/A:435,312 sphere

Changed 18 atom styles  

> color #1/A:435,312 red

> hide #2 cartoons

> hide #2 atoms

> select #2/B:628-684

442 atoms, 454 bonds, 1 model selected  

> select #2/B:628-684

442 atoms, 454 bonds, 1 model selected  

> sequence chain #2/B#2/D

Alignment identifier is 1  

> set bgColor black

> select #1/B:678

7 atoms, 6 bonds, 1 model selected  

> select up

267 atoms, 274 bonds, 1 model selected  

> select up

400 atoms, 402 bonds, 1 model selected  

> select down

267 atoms, 274 bonds, 1 model selected  

> show sel atoms

> style sel sphere

Changed 267 atom styles  

> style sel stick

Changed 267 atom styles  

> style sel stick

Changed 267 atom styles  

> style sel ball

Changed 267 atom styles  

> style sel ball

Changed 267 atom styles  

> style sel sphere

Changed 267 atom styles  

> style sel ball

Changed 267 atom styles  

> style sel stick

Changed 267 atom styles  

> style sel sphere

Changed 267 atom styles  

> style sel stick

Changed 267 atom styles  

> preset "initial styles" sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides licorice/ovals

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> preset cartoons/nucleotides ribbons/slabs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> hide #2

> close

> device snav true

Could not start space navigator.  
  
cannot import name '_spacenavigator' from 'chimerax.spacenavigator'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/spacenavigator/__init__.py)  

> open 3OUW

Summary of feedback from opening 3OUW fetched from pdb  
---  
note | Fetching compressed mmCIF 3ouw from
http://files.rcsb.org/download/3ouw.cif  
  
3ouw title:  
Structure of beta-catenin with Lef-1 [more info...]  
  
Chain information for 3ouw #1  
---  
Chain | Description  
A | Catenin beta-1  
B | Lymphoid enhancer-binding factor 1  
  
  

> open 1G3J

Summary of feedback from opening 1G3J fetched from pdb  
---  
note | Fetching compressed mmCIF 1g3j from
http://files.rcsb.org/download/1g3j.cif  
  
1g3j title:  
Crystal structure of the XTCF3-CBD/β-catenin armadillo repeat complex [more
info...]  
  
Chain information for 1g3j #2  
---  
Chain | Description  
A C | β-catenin armadillo repeat region  
B D | TCF3-CBD (catenin binding domain)  
  
1g3j mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
  
  

> hide atoms

> show ribbons

> hide solvent

> hide #2 /C/D target c

> set bgColor grey

> color #1 /A hot pink

> color #1 /B cyan

> color #2 /A rgb(255,255,0)

> color #2 /B rgb(255,0,0)

> mmaker #2:134-664 to #1:167-662

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 3ouw, chain A (#1) with 1g3j, chain A (#2), sequence alignment
score = 2415.5  
RMSD between 274 pruned atom pairs is 0.981 angstroms; (across all 484 pairs:
3.000)  
  

> cartoon style #1 #2 width 3 thickness 2

> cartoon style #1 #2 width 3

> cartoon style #1 #2 thickness 1

> show #1/A :cys #2/A :cys

> style #1/A :cys #2/A :cys sphere

Changed 132 atom styles  

> color #1/A :cys #2/A :cys blue

> show #1/A:435,312 #2/A:435,312

> color #1/A:435,312 #2/A:435,312 red

> style #1/A:435,312 #2/A:435,312 sphere

Changed 36 atom styles  

> show #2/B:16,17,23,24,26,28,29

> color #2/B:16,17,23,24,26,28,29 green

> style #2/B:16,17,23,24,26,28,29 sphere

Changed 61 atom styles  

> show #1/B:21,22,24 #2/B:18,19,21

> color #1/B:21,22,24 #2/B:18,19,21 cyan

> style #1/B:21,22,24 #2/B:18,19,21 sphere

Changed 54 atom styles  

> select #2/B:2-52

286 atoms, 285 bonds, 1 pseudobond, 2 models selected  

> sequence chain #2/B#2/D

Alignment identifier is 1  

> set bgColor white

> set bgColor black

> style sel stick

Changed 10 atom styles  

> show sel cartoons

> style sel ball

Changed 10 atom styles  

> style sel sphere

Changed 10 atom styles  

> style sel stick

Changed 10 atom styles  

> show sel atoms

> style sel stick

Changed 10 atom styles  

> style sel ball

Changed 10 atom styles  

> show #2/B:22

> stype #2/B:22 ball

Unknown command: stype #2/B:22 ball  

> style #2/B:22 sphere

Changed 5 atom styles  

> device snav true

Could not start space navigator.  
  
cannot import name '_spacenavigator' from 'chimerax.spacenavigator'
(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/spacenavigator/__init__.py)  




OpenGL version: 4.1 ATI-3.8.24
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → General Controls
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Could not start space navigator

comment:2 by Tom Goddard, 5 years ago

Resolution: → duplicate
Status: assigned → closed

Fixed a week ago. Get current ChimeraX release candidate.

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